Starting phenix.real_space_refine on Thu Feb 15 11:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmf_10519/02_2024/6tmf_10519_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 8 7.16 5 Zn 4 6.06 5 P 1491 5.49 5 Mg 29 5.21 5 S 136 5.16 5 C 35415 2.51 5 N 12110 2.21 5 O 16256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 9": "OD1" <-> "OD2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 180": "OD1" <-> "OD2" Residue "F ARG 189": "NH1" <-> "NH2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 92": "NH1" <-> "NH2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ASP 63": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ARG 29": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N ASP 119": "OD1" <-> "OD2" Residue "N ARG 135": "NH1" <-> "NH2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O ASP 98": "OD1" <-> "OD2" Residue "O ARG 141": "NH1" <-> "NH2" Residue "O GLU 143": "OE1" <-> "OE2" Residue "P ASP 3": "OD1" <-> "OD2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 122": "OE1" <-> "OE2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 40": "OD1" <-> "OD2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 106": "OE1" <-> "OE2" Residue "U ARG 111": "NH1" <-> "NH2" Residue "V GLU 24": "OE1" <-> "OE2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V ARG 43": "NH1" <-> "NH2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 65": "OD1" <-> "OD2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "X PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 22": "OD1" <-> "OD2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ASP 52": "OD1" <-> "OD2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 85": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "d ARG 28": "NH1" <-> "NH2" Residue "d TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 129": "OD1" <-> "OD2" Residue "d ARG 144": "NH1" <-> "NH2" Residue "d TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 194": "OD1" <-> "OD2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "d ARG 293": "NH1" <-> "NH2" Residue "d ARG 301": "NH1" <-> "NH2" Residue "d GLU 315": "OE1" <-> "OE2" Residue "d GLU 323": "OE1" <-> "OE2" Residue "d ASP 355": "OD1" <-> "OD2" Residue "d GLU 367": "OE1" <-> "OE2" Residue "d GLU 426": "OE1" <-> "OE2" Residue "d PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 454": "OE1" <-> "OE2" Residue "d GLU 477": "OE1" <-> "OE2" Residue "d ASP 519": "OD1" <-> "OD2" Residue "d ASP 524": "OD1" <-> "OD2" Residue "d ARG 565": "NH1" <-> "NH2" Residue "d ASP 567": "OD1" <-> "OD2" Residue "d ARG 584": "NH1" <-> "NH2" Residue "d GLU 588": "OE1" <-> "OE2" Residue "d ARG 589": "NH1" <-> "NH2" Residue "d ASP 591": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 65449 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 31920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1485, 31920 Classifications: {'RNA': 1485} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 80, 'rna3p_pur': 724, 'rna3p_pyr': 568} Link IDs: {'rna2p': 192, 'rna3p': 1292} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1571 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1526 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1520 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1476 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain: "F" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1963 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1721 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 116} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1704 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "J" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1022 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1040 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "M" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 819 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "N" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1005 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "O" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1131 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "P" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1109 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "Q" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 459 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "R" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 913 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "T" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 540 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "U" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 949 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "V" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1218 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 10, 'TRANS': 138} Chain: "W" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 435 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "X" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Y" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 475 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "Z" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "a" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 936 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 113} Chain: "c" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 351 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "d" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4622 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 561} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Unusual residues: {' MG': 27} Classifications: {'undetermined': 27} Link IDs: {None: 26} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' MG': 2, 'ANP': 2, 'SF4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 51657 SG CYS Q 21 66.016 80.359 167.613 1.00 15.56 S ATOM 51681 SG CYS Q 24 68.182 81.194 164.493 1.00 16.72 S ATOM 51794 SG CYS Q 39 67.682 84.251 166.328 1.00 14.61 S ATOM 51821 SG CYS Q 42 64.221 83.210 164.830 1.00 14.58 S ATOM 56984 SG CYS W 28 21.118 149.447 123.456 1.00 21.12 S ATOM 57005 SG CYS W 31 17.177 149.557 121.586 1.00 26.33 S ATOM 57164 SG CYS W 51 20.970 148.871 119.979 1.00 20.62 S ATOM 57186 SG CYS W 54 20.119 151.508 121.372 1.00 24.40 S ATOM 56845 SG CYS W 10 32.289 142.348 117.986 1.00 15.94 S ATOM 56864 SG CYS W 13 34.487 141.687 115.183 1.00 18.75 S ATOM 57070 SG CYS W 39 35.746 140.931 118.147 1.00 14.20 S ATOM 57091 SG CYS W 42 35.786 144.290 118.135 1.00 13.59 S ATOM 58171 SG CYS Y 20 51.623 203.188 111.393 1.00 28.53 S ATOM 58314 SG CYS Y 39 53.806 201.441 108.740 1.00 25.44 S ATOM 58335 SG CYS Y 42 55.653 203.728 110.361 1.00 26.40 S ATOM 60910 SG CYS d 24 104.529 92.014 93.381 1.00 14.47 S ATOM 61113 SG CYS d 51 102.994 87.629 87.553 1.00 13.27 S ATOM 61149 SG CYS d 57 104.165 93.972 86.257 1.00 12.11 S ATOM 61131 SG CYS d 54 98.987 92.317 90.098 1.00 11.12 S ATOM 61180 SG CYS d 61 108.301 99.729 82.994 1.00 15.15 S ATOM 60807 SG CYS d 11 114.710 96.960 82.905 1.00 21.30 S Time building chain proxies: 26.26, per 1000 atoms: 0.40 Number of scatterers: 65449 At special positions: 0 Unit cell: (145.256, 214.632, 247.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 8 26.01 S 136 16.00 P 1491 15.00 Mg 29 11.99 O 16256 8.00 N 12110 7.00 C 35415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.88 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 d 601 " pdb="FE2 SF4 d 601 " - pdb=" SG CYS d 51 " pdb="FE4 SF4 d 601 " - pdb=" SG CYS d 54 " pdb="FE1 SF4 d 601 " - pdb=" SG CYS d 24 " pdb="FE3 SF4 d 601 " - pdb=" SG CYS d 57 " pdb=" SF4 d 602 " pdb="FE3 SF4 d 602 " - pdb=" SG CYS d 61 " pdb="FE4 SF4 d 602 " - pdb=" SG CYS d 11 " pdb="FE2 SF4 d 602 " - pdb=" SG CYS d 16 " pdb="FE1 SF4 d 602 " - pdb=" SG CYS d 20 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN Q 101 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 39 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 24 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 21 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 42 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 54 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 51 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 28 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 31 " pdb=" ZN W 102 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 13 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 10 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 102 " - pdb=" SG CYS W 39 " pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 42 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 20 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 39 " Number of angles added : 18 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 43 sheets defined 31.9% alpha, 15.7% beta 521 base pairs and 833 stacking pairs defined. Time for finding SS restraints: 25.92 Creating SS restraints... Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'B' and resid 73 through 86 Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 160 through 178 removed outlier: 6.110A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 60 through 72 Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'D' and resid 44 through 47 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 135 through 155 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 166 through 173 Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 59 through 68 Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'G' and resid 3 through 8 removed outlier: 3.895A pdb=" N GLU G 8 " --> pdb=" O ARG G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 20 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 162 through 171 Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.373A pdb=" N ASN G 202 " --> pdb=" O LEU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 removed outlier: 3.582A pdb=" N GLU G 211 " --> pdb=" O PRO G 208 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR G 214 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 40 through 43 No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 31 through 36 Proline residue: I 35 - end of helix No H-bonds generated for 'chain 'I' and resid 31 through 36' Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 81 through 83 No H-bonds generated for 'chain 'I' and resid 81 through 83' Processing helix chain 'I' and resid 97 through 113 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 154 through 173 Processing helix chain 'I' and resid 180 through 193 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'J' and resid 6 through 19 Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'K' and resid 25 through 27 No H-bonds generated for 'chain 'K' and resid 25 through 27' Processing helix chain 'K' and resid 87 through 92 Processing helix chain 'K' and resid 114 through 117 No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'L' and resid 33 through 35 No H-bonds generated for 'chain 'L' and resid 33 through 35' Processing helix chain 'L' and resid 39 through 52 Proline residue: L 48 - end of helix Processing helix chain 'L' and resid 54 through 59 removed outlier: 4.849A pdb=" N GLY L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 90 Processing helix chain 'L' and resid 93 through 102 Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'M' and resid 13 through 29 Processing helix chain 'M' and resid 79 through 87 Processing helix chain 'N' and resid 46 through 49 No H-bonds generated for 'chain 'N' and resid 46 through 49' Processing helix chain 'N' and resid 53 through 56 No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 59 through 75 removed outlier: 6.339A pdb=" N ILE N 64 " --> pdb=" O TYR N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 110 Processing helix chain 'O' and resid 13 through 26 removed outlier: 3.972A pdb=" N SER O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 93 through 96 No H-bonds generated for 'chain 'O' and resid 93 through 96' Processing helix chain 'O' and resid 134 through 138 Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 34 through 44 Processing helix chain 'P' and resid 52 through 54 No H-bonds generated for 'chain 'P' and resid 52 through 54' Processing helix chain 'P' and resid 57 through 68 Processing helix chain 'P' and resid 71 through 73 No H-bonds generated for 'chain 'P' and resid 71 through 73' Processing helix chain 'P' and resid 96 through 113 Processing helix chain 'P' and resid 116 through 123 Processing helix chain 'Q' and resid 40 through 50 Proline residue: Q 48 - end of helix Processing helix chain 'R' and resid 30 through 43 Processing helix chain 'R' and resid 47 through 56 Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 71 through 77 Processing helix chain 'R' and resid 86 through 104 Processing helix chain 'R' and resid 109 through 132 Processing helix chain 'R' and resid 143 through 150 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'T' and resid 21 through 23 No H-bonds generated for 'chain 'T' and resid 21 through 23' Processing helix chain 'T' and resid 28 through 37 Processing helix chain 'T' and resid 44 through 63 Processing helix chain 'U' and resid 14 through 19 Processing helix chain 'U' and resid 22 through 28 Processing helix chain 'U' and resid 31 through 39 Processing helix chain 'U' and resid 43 through 56 Processing helix chain 'U' and resid 97 through 99 No H-bonds generated for 'chain 'U' and resid 97 through 99' Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'V' and resid 10 through 22 removed outlier: 4.359A pdb=" N GLU V 22 " --> pdb=" O LYS V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 64 Processing helix chain 'V' and resid 70 through 77 Processing helix chain 'V' and resid 96 through 108 Processing helix chain 'V' and resid 123 through 141 Processing helix chain 'V' and resid 145 through 148 No H-bonds generated for 'chain 'V' and resid 145 through 148' Processing helix chain 'W' and resid 40 through 44 Processing helix chain 'X' and resid 33 through 43 Processing helix chain 'X' and resid 75 through 81 Processing helix chain 'X' and resid 84 through 90 Processing helix chain 'b' and resid 13 through 27 removed outlier: 3.504A pdb=" N GLU b 17 " --> pdb=" O ALA b 13 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 45 Processing helix chain 'b' and resid 63 through 66 No H-bonds generated for 'chain 'b' and resid 63 through 66' Processing helix chain 'b' and resid 70 through 72 No H-bonds generated for 'chain 'b' and resid 70 through 72' Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 108 through 121 removed outlier: 4.256A pdb=" N ASP b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 8 No H-bonds generated for 'chain 'c' and resid 5 through 8' Processing helix chain 'c' and resid 16 through 35 Processing helix chain 'd' and resid 19 through 22 No H-bonds generated for 'chain 'd' and resid 19 through 22' Processing helix chain 'd' and resid 25 through 29 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 112 through 120 Processing helix chain 'd' and resid 137 through 143 Processing helix chain 'd' and resid 148 through 156 Processing helix chain 'd' and resid 169 through 175 removed outlier: 4.443A pdb=" N PHE d 175 " --> pdb=" O TYR d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 187 Processing helix chain 'd' and resid 193 through 200 Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 215 through 228 Processing helix chain 'd' and resid 245 through 258 Processing helix chain 'd' and resid 271 through 275 Processing helix chain 'd' and resid 300 through 309 Processing helix chain 'd' and resid 382 through 389 Processing helix chain 'd' and resid 421 through 428 Processing helix chain 'd' and resid 438 through 442 Processing helix chain 'd' and resid 462 through 475 Processing helix chain 'd' and resid 492 through 509 Processing helix chain 'd' and resid 520 through 526 Processing helix chain 'd' and resid 549 through 558 Processing helix chain 'd' and resid 581 through 589 Processing sheet with id= A, first strand: chain 'B' and resid 137 through 140 removed outlier: 6.544A pdb=" N LEU B 151 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 140 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE B 153 " --> pdb=" O VAL B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.878A pdb=" N VAL B 41 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 32 through 38 Processing sheet with id= D, first strand: chain 'C' and resid 142 through 149 Processing sheet with id= E, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.090A pdb=" N GLN D 73 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE D 86 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N LYS D 85 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N ALA D 196 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS D 87 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS D 120 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 24 through 26 Processing sheet with id= G, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= H, first strand: chain 'F' and resid 42 through 44 Processing sheet with id= I, first strand: chain 'F' and resid 89 through 93 Processing sheet with id= J, first strand: chain 'F' and resid 123 through 126 removed outlier: 4.754A pdb=" N GLU F 175 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS F 167 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL F 173 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 130 through 133 Processing sheet with id= L, first strand: chain 'F' and resid 230 through 234 removed outlier: 6.874A pdb=" N TYR F 184 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR F 214 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL F 202 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 212 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 88 through 96 removed outlier: 6.501A pdb=" N ALA G 81 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL G 58 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 83 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN G 56 " --> pdb=" O GLY G 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 138 through 142 Processing sheet with id= O, first strand: chain 'H' and resid 15 through 21 removed outlier: 3.699A pdb=" N GLY H 65 " --> pdb=" O ASN H 120 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS H 122 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE H 63 " --> pdb=" O LYS H 122 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL H 124 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU H 61 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 83 through 87 Processing sheet with id= Q, first strand: chain 'I' and resid 134 through 141 Processing sheet with id= R, first strand: chain 'J' and resid 24 through 27 Processing sheet with id= S, first strand: chain 'J' and resid 71 through 74 removed outlier: 6.846A pdb=" N ILE J 103 " --> pdb=" O ILE J 126 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR J 128 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE J 101 " --> pdb=" O TYR J 128 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 79 through 81 Processing sheet with id= U, first strand: chain 'K' and resid 71 through 73 Processing sheet with id= V, first strand: chain 'K' and resid 43 through 49 removed outlier: 6.575A pdb=" N LYS K 45 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU K 58 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE K 47 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL K 56 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR K 49 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG K 54 " --> pdb=" O THR K 49 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 3 through 9 Processing sheet with id= X, first strand: chain 'M' and resid 94 through 101 removed outlier: 4.609A pdb=" N LYS M 70 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 43 through 50 Processing sheet with id= Z, first strand: chain 'N' and resid 40 through 45 removed outlier: 6.520A pdb=" N ILE N 32 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG N 43 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE N 30 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER N 45 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR N 28 " --> pdb=" O SER N 45 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY N 80 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA N 19 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS N 82 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE N 21 " --> pdb=" O HIS N 82 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS N 84 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER N 23 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG N 86 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 82 through 87 removed outlier: 6.233A pdb=" N GLN O 76 " --> pdb=" O VAL O 54 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL O 54 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS O 128 " --> pdb=" O ILE O 104 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU O 106 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL O 126 " --> pdb=" O GLU O 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 61 through 68 removed outlier: 3.744A pdb=" N SER S 39 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU S 49 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL S 37 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ARG S 51 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLY S 35 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 15.390A pdb=" N TYR S 53 " --> pdb=" O PHE S 33 " (cutoff:3.500A) removed outlier: 16.554A pdb=" N PHE S 33 " --> pdb=" O TYR S 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA S 103 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA S 88 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL S 101 " --> pdb=" O ALA S 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'U' and resid 64 through 66 removed outlier: 4.381A pdb=" N ILE U 64 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 79 through 81 removed outlier: 3.935A pdb=" N HIS V 89 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'V' and resid 111 through 113 Processing sheet with id= AF, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AG, first strand: chain 'X' and resid 2 through 11 removed outlier: 6.786A pdb=" N TYR X 20 " --> pdb=" O ARG X 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET X 8 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU X 18 " --> pdb=" O MET X 8 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU X 10 " --> pdb=" O ARG X 16 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG X 16 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS X 70 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE X 53 " --> pdb=" O LYS X 70 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR X 72 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL X 51 " --> pdb=" O TYR X 72 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Y' and resid 15 through 19 Processing sheet with id= AI, first strand: chain 'a' and resid 39 through 45 removed outlier: 3.512A pdb=" N GLU a 12 " --> pdb=" O LYS a 27 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG a 29 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL a 10 " --> pdb=" O ARG a 29 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'b' and resid 32 through 34 removed outlier: 3.886A pdb=" N ILE b 101 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU b 50 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE b 53 " --> pdb=" O PRO b 76 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE b 78 " --> pdb=" O ILE b 53 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'd' and resid 2 through 6 Processing sheet with id= AL, first strand: chain 'd' and resid 34 through 37 Processing sheet with id= AM, first strand: chain 'd' and resid 284 through 287 removed outlier: 6.813A pdb=" N LYS d 89 " --> pdb=" O GLY d 292 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL d 294 " --> pdb=" O LYS d 89 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE d 91 " --> pdb=" O VAL d 294 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE d 88 " --> pdb=" O LYS d 84 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS d 84 " --> pdb=" O PHE d 88 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU d 90 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG d 82 " --> pdb=" O LEU d 90 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'd' and resid 280 through 282 removed outlier: 6.493A pdb=" N VAL d 264 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL d 104 " --> pdb=" O VAL d 264 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL d 266 " --> pdb=" O VAL d 104 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL d 163 " --> pdb=" O ILE d 235 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP d 237 " --> pdb=" O VAL d 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS d 165 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'd' and resid 540 through 542 removed outlier: 8.243A pdb=" N GLY d 541 " --> pdb=" O ASP d 355 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN d 357 " --> pdb=" O GLY d 541 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN d 357 " --> pdb=" O LYS d 351 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS d 351 " --> pdb=" O GLN d 357 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'd' and resid 529 through 533 removed outlier: 6.186A pdb=" N THR d 513 " --> pdb=" O ILE d 371 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE d 373 " --> pdb=" O THR d 513 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE d 515 " --> pdb=" O ILE d 373 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY d 375 " --> pdb=" O ILE d 515 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU d 483 " --> pdb=" O PHE d 514 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 564 through 566 1128 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1391 hydrogen bonds 2300 hydrogen bond angles 0 basepair planarities 521 basepair parallelities 833 stacking parallelities Total time for adding SS restraints: 46.27 Time building geometry restraints manager: 28.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.38: 26426 1.38 - 1.61: 42998 1.61 - 1.83: 368 1.83 - 2.05: 0 2.05 - 2.28: 24 Bond restraints: 69816 Sorted by residual: bond pdb=" C1' ANP d 603 " pdb=" C2' ANP d 603 " ideal model delta sigma weight residual 1.542 1.291 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' ANP d 605 " pdb=" C2' ANP d 605 " ideal model delta sigma weight residual 1.542 1.296 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' ANP d 605 " pdb=" O4' ANP d 605 " ideal model delta sigma weight residual 1.394 1.611 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1' ANP d 603 " pdb=" O4' ANP d 603 " ideal model delta sigma weight residual 1.394 1.609 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C4' ANP d 603 " pdb=" O4' ANP d 603 " ideal model delta sigma weight residual 1.431 1.296 0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 69811 not shown) Histogram of bond angle deviations from ideal: 73.18 - 86.99: 24 86.99 - 100.80: 204 100.80 - 114.61: 52788 114.61 - 128.43: 45690 128.43 - 142.24: 2879 Bond angle restraints: 101585 Sorted by residual: angle pdb=" N LYS O 5 " pdb=" CA LYS O 5 " pdb=" C LYS O 5 " ideal model delta sigma weight residual 110.10 122.13 -12.03 1.49e+00 4.50e-01 6.52e+01 angle pdb=" N GLY c 35 " pdb=" CA GLY c 35 " pdb=" C GLY c 35 " ideal model delta sigma weight residual 112.73 122.28 -9.55 1.20e+00 6.94e-01 6.33e+01 angle pdb=" N GLY E 63 " pdb=" CA GLY E 63 " pdb=" C GLY E 63 " ideal model delta sigma weight residual 113.18 130.04 -16.86 2.37e+00 1.78e-01 5.06e+01 angle pdb=" N ASP G 86 " pdb=" CA ASP G 86 " pdb=" C ASP G 86 " ideal model delta sigma weight residual 110.80 96.32 14.48 2.13e+00 2.20e-01 4.62e+01 angle pdb=" C ALA O 6 " pdb=" N PRO O 7 " pdb=" CA PRO O 7 " ideal model delta sigma weight residual 119.84 128.34 -8.50 1.25e+00 6.40e-01 4.62e+01 ... (remaining 101580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 40267 35.92 - 71.85: 4067 71.85 - 107.77: 443 107.77 - 143.70: 16 143.70 - 179.62: 29 Dihedral angle restraints: 44822 sinusoidal: 32850 harmonic: 11972 Sorted by residual: dihedral pdb=" O4' U A 158 " pdb=" C1' U A 158 " pdb=" N1 U A 158 " pdb=" C2 U A 158 " ideal model delta sinusoidal sigma weight residual 200.00 21.67 178.33 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 422 " pdb=" C1' U A 422 " pdb=" N1 U A 422 " pdb=" C2 U A 422 " ideal model delta sinusoidal sigma weight residual 200.00 23.69 176.31 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 172 " pdb=" C1' U A 172 " pdb=" N1 U A 172 " pdb=" C2 U A 172 " ideal model delta sinusoidal sigma weight residual 200.00 32.30 167.70 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 44819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 11138 0.109 - 0.218: 1229 0.218 - 0.327: 59 0.327 - 0.436: 11 0.436 - 0.544: 1 Chirality restraints: 12438 Sorted by residual: chirality pdb=" CA LYS O 5 " pdb=" N LYS O 5 " pdb=" C LYS O 5 " pdb=" CB LYS O 5 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA ASN P 19 " pdb=" N ASN P 19 " pdb=" C ASN P 19 " pdb=" CB ASN P 19 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA LYS d 136 " pdb=" N LYS d 136 " pdb=" C LYS d 136 " pdb=" CB LYS d 136 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 12435 not shown) Planarity restraints: 7352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 830 " 0.064 2.00e-02 2.50e+03 6.25e-02 8.78e+01 pdb=" N1 C A 830 " -0.042 2.00e-02 2.50e+03 pdb=" C2 C A 830 " -0.146 2.00e-02 2.50e+03 pdb=" O2 C A 830 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C A 830 " 0.025 2.00e-02 2.50e+03 pdb=" C4 C A 830 " -0.024 2.00e-02 2.50e+03 pdb=" N4 C A 830 " 0.047 2.00e-02 2.50e+03 pdb=" C5 C A 830 " 0.008 2.00e-02 2.50e+03 pdb=" C6 C A 830 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 352 " 0.021 2.00e-02 2.50e+03 5.52e-02 6.84e+01 pdb=" N1 C A 352 " -0.008 2.00e-02 2.50e+03 pdb=" C2 C A 352 " -0.139 2.00e-02 2.50e+03 pdb=" O2 C A 352 " 0.076 2.00e-02 2.50e+03 pdb=" N3 C A 352 " 0.017 2.00e-02 2.50e+03 pdb=" C4 C A 352 " -0.021 2.00e-02 2.50e+03 pdb=" N4 C A 352 " 0.027 2.00e-02 2.50e+03 pdb=" C5 C A 352 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C A 352 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1000 " 0.009 2.00e-02 2.50e+03 5.11e-02 5.88e+01 pdb=" N1 C A1000 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A1000 " 0.124 2.00e-02 2.50e+03 pdb=" O2 C A1000 " -0.070 2.00e-02 2.50e+03 pdb=" N3 C A1000 " -0.026 2.00e-02 2.50e+03 pdb=" C4 C A1000 " 0.035 2.00e-02 2.50e+03 pdb=" N4 C A1000 " -0.017 2.00e-02 2.50e+03 pdb=" C5 C A1000 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C A1000 " -0.022 2.00e-02 2.50e+03 ... (remaining 7349 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 249 2.38 - 3.01: 36119 3.01 - 3.64: 113812 3.64 - 4.27: 190755 4.27 - 4.90: 267573 Nonbonded interactions: 608508 Sorted by model distance: nonbonded pdb=" O2G ANP d 605 " pdb="MG MG d 606 " model vdw 1.750 2.170 nonbonded pdb=" OP2 G A1051 " pdb="MG MG A1520 " model vdw 1.797 2.170 nonbonded pdb=" O GLY d 53 " pdb=" S1 SF4 d 601 " model vdw 1.824 3.400 nonbonded pdb=" OP2 G A 94 " pdb="MG MG A1511 " model vdw 1.862 2.170 nonbonded pdb=" O GLU D 173 " pdb=" O LYS D 176 " model vdw 1.890 3.040 ... (remaining 608503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.380 Check model and map are aligned: 0.710 Set scattering table: 0.460 Process input model: 191.280 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.273 69816 Z= 1.050 Angle : 1.110 16.861 101585 Z= 0.563 Chirality : 0.071 0.544 12438 Planarity : 0.007 0.089 7352 Dihedral : 22.992 179.620 37138 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.51 % Favored : 89.98 % Rotamer: Outliers : 0.73 % Allowed : 5.65 % Favored : 93.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.11), residues: 4112 helix: -2.13 (0.11), residues: 1460 sheet: -2.09 (0.17), residues: 763 loop : -2.74 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP V 76 HIS 0.022 0.002 HIS I 46 PHE 0.035 0.003 PHE V 34 TYR 0.033 0.003 TYR d 263 ARG 0.025 0.001 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 917 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLN cc_start: 0.7670 (tt0) cc_final: 0.7401 (tt0) REVERT: C 47 PHE cc_start: 0.6360 (m-80) cc_final: 0.6125 (m-10) REVERT: F 224 ASP cc_start: 0.7780 (m-30) cc_final: 0.7564 (m-30) REVERT: M 1 MET cc_start: 0.4262 (tpt) cc_final: 0.3170 (tmm) REVERT: P 51 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7291 (mmmt) REVERT: T 1 MET cc_start: 0.2673 (mpp) cc_final: 0.2061 (mpp) REVERT: Y 10 MET cc_start: 0.8026 (mmm) cc_final: 0.7781 (mmm) REVERT: Y 25 ASN cc_start: 0.6761 (p0) cc_final: 0.6551 (p0) REVERT: a 52 ASP cc_start: 0.7071 (m-30) cc_final: 0.6510 (m-30) REVERT: b 18 LYS cc_start: -0.1022 (tmtt) cc_final: -0.1617 (tptp) outliers start: 26 outliers final: 14 residues processed: 938 average time/residue: 1.9321 time to fit residues: 2243.8453 Evaluate side-chains 657 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 643 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 37 ILE Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 366 LYS Chi-restraints excluded: chain d residue 521 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 466 optimal weight: 3.9990 chunk 419 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 282 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 433 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 502 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN C 87 ASN C 123 ASN C 168 GLN D 80 GLN D 81 ASN E 106 GLN E 135 GLN F 143 HIS F 148 HIS F 192 ASN G 56 GLN G 174 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 51 HIS ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN K 83 ASN K 88 GLN L 5 GLN L 117 HIS L 131 GLN M 84 GLN P 21 GLN R 57 GLN R 78 ASN T 30 HIS V 103 GLN Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN d 70 ASN d 86 ASN d 126 ASN d 131 ASN d 167 GLN d 219 GLN d 282 HIS d 404 GLN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 450 HIS d 456 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 69816 Z= 0.180 Angle : 0.648 13.272 101585 Z= 0.333 Chirality : 0.040 0.331 12438 Planarity : 0.005 0.056 7352 Dihedral : 23.878 179.937 28470 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.83 % Favored : 93.04 % Rotamer: Outliers : 3.31 % Allowed : 15.65 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 4112 helix: 0.01 (0.13), residues: 1402 sheet: -1.54 (0.18), residues: 731 loop : -1.89 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 438 HIS 0.006 0.001 HIS I 46 PHE 0.019 0.002 PHE b 9 TYR 0.031 0.001 TYR b 77 ARG 0.008 0.001 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 790 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 91 ASP cc_start: 0.7304 (m-30) cc_final: 0.7090 (m-30) REVERT: F 88 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6383 (mtt) REVERT: G 73 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7489 (mmt180) REVERT: H 111 THR cc_start: 0.8365 (p) cc_final: 0.7873 (m) REVERT: L 46 MET cc_start: 0.7505 (mtt) cc_final: 0.7236 (mtt) REVERT: L 131 GLN cc_start: 0.8401 (tt0) cc_final: 0.8170 (tt0) REVERT: M 1 MET cc_start: 0.4164 (tpt) cc_final: 0.3106 (tmm) REVERT: O 123 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7802 (mtp85) REVERT: R 56 ASP cc_start: 0.8271 (m-30) cc_final: 0.8057 (m-30) REVERT: T 1 MET cc_start: 0.2073 (mpp) cc_final: 0.1610 (mpp) REVERT: U 71 MET cc_start: 0.8030 (tpt) cc_final: 0.7827 (tpt) REVERT: Y 10 MET cc_start: 0.7978 (mmm) cc_final: 0.7697 (tpp) REVERT: a 1 MET cc_start: 0.2680 (tmt) cc_final: 0.2364 (ppp) REVERT: b 73 LYS cc_start: 0.1064 (OUTLIER) cc_final: -0.0149 (ttpp) outliers start: 117 outliers final: 44 residues processed: 837 average time/residue: 1.6545 time to fit residues: 1744.1928 Evaluate side-chains 730 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 683 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain U residue 22 LEU Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain V residue 144 LEU Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain d residue 528 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 417 optimal weight: 3.9990 chunk 341 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 503 optimal weight: 0.0770 chunk 543 optimal weight: 0.9980 chunk 448 optimal weight: 2.9990 chunk 498 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 403 optimal weight: 5.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN E 75 GLN E 120 GLN E 123 GLN F 192 ASN G 55 ASN G 113 ASN H 13 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN K 88 GLN O 76 GLN P 17 ASN P 21 GLN R 57 GLN R 78 ASN U 45 GLN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN d 86 ASN d 404 GLN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 448 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69816 Z= 0.231 Angle : 0.624 10.700 101585 Z= 0.323 Chirality : 0.040 0.342 12438 Planarity : 0.005 0.063 7352 Dihedral : 23.716 179.611 28456 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 4.52 % Allowed : 17.89 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4112 helix: 0.55 (0.14), residues: 1399 sheet: -1.19 (0.19), residues: 730 loop : -1.55 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 438 HIS 0.005 0.001 HIS I 46 PHE 0.016 0.002 PHE J 97 TYR 0.020 0.001 TYR d 263 ARG 0.009 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 711 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3262 (tmm) cc_final: 0.2707 (tmm) REVERT: D 70 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8841 (mt) REVERT: H 111 THR cc_start: 0.8324 (p) cc_final: 0.7836 (m) REVERT: L 131 GLN cc_start: 0.8481 (tt0) cc_final: 0.8233 (tt0) REVERT: M 1 MET cc_start: 0.4327 (tpt) cc_final: 0.3154 (tmm) REVERT: O 123 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7756 (mtp85) REVERT: R 56 ASP cc_start: 0.8421 (m-30) cc_final: 0.8199 (m-30) REVERT: T 25 SER cc_start: 0.8433 (p) cc_final: 0.8198 (p) REVERT: T 26 ARG cc_start: 0.7540 (ttt-90) cc_final: 0.7274 (ttt-90) REVERT: U 71 MET cc_start: 0.8096 (tpt) cc_final: 0.7894 (tpt) REVERT: Y 10 MET cc_start: 0.7912 (mmm) cc_final: 0.7656 (mmp) REVERT: d 367 GLU cc_start: 0.4813 (OUTLIER) cc_final: 0.4344 (mp0) outliers start: 160 outliers final: 70 residues processed: 801 average time/residue: 1.6654 time to fit residues: 1676.7817 Evaluate side-chains 745 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 672 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 86 ASN Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 367 GLU Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 497 optimal weight: 1.9990 chunk 378 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 337 optimal weight: 10.0000 chunk 504 optimal weight: 8.9990 chunk 534 optimal weight: 7.9990 chunk 263 optimal weight: 0.0040 chunk 478 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 95 GLN D 81 ASN E 37 ASN E 75 GLN E 120 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN K 83 ASN K 88 GLN P 21 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 69816 Z= 0.211 Angle : 0.603 10.324 101585 Z= 0.312 Chirality : 0.039 0.336 12438 Planarity : 0.005 0.056 7352 Dihedral : 23.661 179.723 28455 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.05 % Favored : 92.85 % Rotamer: Outliers : 4.10 % Allowed : 20.54 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4112 helix: 0.77 (0.14), residues: 1389 sheet: -0.98 (0.19), residues: 723 loop : -1.43 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 438 HIS 0.005 0.001 HIS I 46 PHE 0.016 0.001 PHE V 34 TYR 0.016 0.001 TYR d 263 ARG 0.009 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 719 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7209 (mt) REVERT: D 70 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8829 (mt) REVERT: E 123 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: G 73 ARG cc_start: 0.7689 (mmt-90) cc_final: 0.7316 (mmt180) REVERT: H 111 THR cc_start: 0.8329 (p) cc_final: 0.7901 (m) REVERT: J 4 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7266 (mt) REVERT: J 34 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: J 62 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7695 (ttt-90) REVERT: L 131 GLN cc_start: 0.8477 (tt0) cc_final: 0.8199 (tt0) REVERT: M 1 MET cc_start: 0.4169 (tpt) cc_final: 0.3336 (tmm) REVERT: O 123 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: R 56 ASP cc_start: 0.8377 (m-30) cc_final: 0.8151 (m-30) REVERT: S 66 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8180 (mtm180) REVERT: T 25 SER cc_start: 0.8336 (p) cc_final: 0.8057 (p) REVERT: T 26 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.7171 (ttt90) REVERT: Y 10 MET cc_start: 0.7915 (mmm) cc_final: 0.7705 (mmp) REVERT: b 73 LYS cc_start: -0.0039 (OUTLIER) cc_final: -0.0559 (ttpp) outliers start: 145 outliers final: 72 residues processed: 791 average time/residue: 1.6456 time to fit residues: 1647.2840 Evaluate side-chains 751 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 671 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain R residue 57 GLN Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 86 ASN Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 445 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 397 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 369 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 479 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 37 ASN E 75 GLN F 121 ASN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN J 64 GLN K 88 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN d 167 GLN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69816 Z= 0.213 Angle : 0.600 10.791 101585 Z= 0.310 Chirality : 0.039 0.335 12438 Planarity : 0.005 0.063 7352 Dihedral : 23.627 179.808 28455 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.02 % Rotamer: Outliers : 4.92 % Allowed : 20.99 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4112 helix: 0.87 (0.14), residues: 1394 sheet: -0.80 (0.19), residues: 710 loop : -1.36 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 438 HIS 0.005 0.001 HIS I 46 PHE 0.017 0.001 PHE V 34 TYR 0.018 0.001 TYR d 263 ARG 0.010 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 705 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3134 (tmm) cc_final: 0.2669 (tpt) REVERT: D 70 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8817 (mt) REVERT: E 123 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: H 111 THR cc_start: 0.8305 (p) cc_final: 0.7898 (m) REVERT: I 206 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: J 4 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7291 (mt) REVERT: K 93 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: L 131 GLN cc_start: 0.8484 (tt0) cc_final: 0.8176 (tt0) REVERT: M 1 MET cc_start: 0.4149 (tpt) cc_final: 0.3316 (tmm) REVERT: M 26 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6450 (tp) REVERT: O 56 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: O 123 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: P 96 THR cc_start: 0.6892 (p) cc_final: 0.6658 (m) REVERT: R 56 ASP cc_start: 0.8402 (m-30) cc_final: 0.8167 (m-30) REVERT: S 50 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: S 66 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: d 99 ASN cc_start: 0.7130 (t0) cc_final: 0.6872 (t160) outliers start: 174 outliers final: 80 residues processed: 805 average time/residue: 1.6415 time to fit residues: 1675.0731 Evaluate side-chains 767 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 677 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 206 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 23 ARG Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 521 SER Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 179 optimal weight: 10.0000 chunk 481 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 535 optimal weight: 3.9990 chunk 444 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 81 ASN E 75 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN J 64 GLN K 88 GLN O 49 GLN R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 69816 Z= 0.327 Angle : 0.660 11.181 101585 Z= 0.341 Chirality : 0.042 0.356 12438 Planarity : 0.005 0.063 7352 Dihedral : 23.658 179.196 28453 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.56 % Favored : 92.34 % Rotamer: Outliers : 4.80 % Allowed : 22.58 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4112 helix: 0.72 (0.14), residues: 1393 sheet: -0.86 (0.19), residues: 721 loop : -1.32 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 438 HIS 0.005 0.001 HIS S 54 PHE 0.025 0.002 PHE V 34 TYR 0.022 0.002 TYR d 263 ARG 0.010 0.001 ARG T 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 691 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: D 42 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6392 (p0) REVERT: D 70 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8828 (mt) REVERT: E 123 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: F 17 ASP cc_start: 0.6921 (p0) cc_final: 0.6711 (p0) REVERT: H 39 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7789 (Cg_exo) REVERT: H 111 THR cc_start: 0.8271 (p) cc_final: 0.7993 (m) REVERT: J 4 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7512 (mt) REVERT: J 62 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7725 (ttt-90) REVERT: K 93 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: L 131 GLN cc_start: 0.8622 (tt0) cc_final: 0.8359 (tt0) REVERT: M 26 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6749 (tp) REVERT: O 56 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: O 123 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7796 (mtp85) REVERT: R 56 ASP cc_start: 0.8458 (m-30) cc_final: 0.8211 (m-30) REVERT: S 50 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7655 (mtm180) REVERT: S 66 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: Y 19 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7445 (mptt) outliers start: 170 outliers final: 91 residues processed: 784 average time/residue: 1.6275 time to fit residues: 1619.4951 Evaluate side-chains 762 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 660 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 43 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 86 ASN Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 279 ASP Chi-restraints excluded: chain d residue 327 MET Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 521 SER Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 515 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 304 optimal weight: 0.0770 chunk 390 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 450 optimal weight: 0.0980 chunk 298 optimal weight: 2.9990 chunk 533 optimal weight: 0.6980 chunk 333 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 192 ASN G 113 ASN ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN R 57 GLN R 78 ASN ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69816 Z= 0.184 Angle : 0.601 11.600 101585 Z= 0.310 Chirality : 0.038 0.332 12438 Planarity : 0.005 0.062 7352 Dihedral : 23.640 179.809 28453 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.13 % Favored : 92.78 % Rotamer: Outliers : 4.07 % Allowed : 23.45 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4112 helix: 0.86 (0.14), residues: 1398 sheet: -0.75 (0.20), residues: 708 loop : -1.26 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 438 HIS 0.004 0.001 HIS d 523 PHE 0.017 0.001 PHE V 34 TYR 0.018 0.001 TYR B 11 ARG 0.011 0.000 ARG T 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 682 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3655 (tmm) cc_final: 0.2969 (tpt) REVERT: D 42 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6629 (p0) REVERT: D 70 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8802 (mt) REVERT: E 123 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: H 111 THR cc_start: 0.8218 (p) cc_final: 0.7966 (m) REVERT: J 4 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7353 (mt) REVERT: L 131 GLN cc_start: 0.8577 (tt0) cc_final: 0.8321 (tt0) REVERT: M 26 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6685 (tp) REVERT: O 123 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7748 (mtp85) REVERT: R 56 ASP cc_start: 0.8460 (m-30) cc_final: 0.8239 (m-30) REVERT: S 50 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7620 (mtm180) REVERT: S 66 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: Y 10 MET cc_start: 0.8175 (mmm) cc_final: 0.7643 (mmp) REVERT: Y 19 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7417 (mptt) REVERT: b 122 MET cc_start: 0.0078 (OUTLIER) cc_final: -0.0258 (ptt) outliers start: 144 outliers final: 79 residues processed: 763 average time/residue: 1.6570 time to fit residues: 1605.0344 Evaluate side-chains 749 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 661 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain Q residue 23 ARG Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 122 MET Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 327 MET Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 521 SER Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 329 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 160 optimal weight: 0.0670 chunk 104 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 75 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN K 88 GLN L 5 GLN O 49 GLN R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 131 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 69816 Z= 0.275 Angle : 0.634 10.975 101585 Z= 0.327 Chirality : 0.041 0.343 12438 Planarity : 0.005 0.064 7352 Dihedral : 23.614 179.831 28453 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.32 % Favored : 92.58 % Rotamer: Outliers : 4.01 % Allowed : 23.99 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4112 helix: 0.78 (0.14), residues: 1406 sheet: -0.75 (0.20), residues: 711 loop : -1.26 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 438 HIS 0.006 0.001 HIS I 48 PHE 0.021 0.002 PHE V 34 TYR 0.020 0.002 TYR D 119 ARG 0.012 0.000 ARG T 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 669 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3897 (tmm) cc_final: 0.3243 (tpt) REVERT: D 42 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6753 (p0) REVERT: D 70 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8818 (mt) REVERT: E 123 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: H 111 THR cc_start: 0.8247 (p) cc_final: 0.7987 (m) REVERT: K 93 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: L 131 GLN cc_start: 0.8622 (tt0) cc_final: 0.8353 (tt0) REVERT: M 26 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6763 (mm) REVERT: O 123 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7746 (mtp85) REVERT: R 56 ASP cc_start: 0.8478 (m-30) cc_final: 0.8253 (m-30) REVERT: S 50 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7552 (mtm180) REVERT: S 66 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8178 (mtm180) REVERT: Y 10 MET cc_start: 0.8199 (mmm) cc_final: 0.7632 (mmp) REVERT: Y 19 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7456 (mptt) REVERT: Z 31 MET cc_start: 0.3199 (mmm) cc_final: 0.2789 (mmp) outliers start: 142 outliers final: 89 residues processed: 754 average time/residue: 1.6651 time to fit residues: 1588.4409 Evaluate side-chains 752 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 655 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 101 MET Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 279 ASP Chi-restraints excluded: chain d residue 327 MET Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 521 SER Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 484 optimal weight: 0.0070 chunk 510 optimal weight: 1.9990 chunk 465 optimal weight: 0.9990 chunk 496 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 448 optimal weight: 0.9990 chunk 469 optimal weight: 10.0000 chunk 494 optimal weight: 0.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 75 GLN F 121 ASN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN J 64 GLN K 88 GLN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 69816 Z= 0.164 Angle : 0.602 10.448 101585 Z= 0.311 Chirality : 0.038 0.325 12438 Planarity : 0.005 0.063 7352 Dihedral : 23.637 179.920 28453 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 3.45 % Allowed : 24.61 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4112 helix: 0.93 (0.14), residues: 1391 sheet: -0.74 (0.20), residues: 701 loop : -1.25 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 438 HIS 0.005 0.001 HIS N 31 PHE 0.016 0.001 PHE J 97 TYR 0.028 0.001 TYR D 119 ARG 0.019 0.000 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 678 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3859 (tmm) cc_final: 0.3192 (tpt) REVERT: C 145 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7783 (ttt90) REVERT: D 42 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6398 (p0) REVERT: D 70 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8814 (mt) REVERT: H 111 THR cc_start: 0.8219 (p) cc_final: 0.7988 (m) REVERT: K 93 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: L 131 GLN cc_start: 0.8593 (tt0) cc_final: 0.8359 (tt0) REVERT: M 26 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6754 (mm) REVERT: O 123 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7746 (mtp85) REVERT: R 56 ASP cc_start: 0.8459 (m-30) cc_final: 0.8242 (m-30) REVERT: S 50 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7613 (mtm180) REVERT: S 66 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8133 (mtm180) REVERT: Y 10 MET cc_start: 0.8176 (mmm) cc_final: 0.7572 (mmp) REVERT: Y 19 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7427 (mptt) REVERT: b 122 MET cc_start: 0.0169 (ptt) cc_final: -0.0151 (ptt) outliers start: 122 outliers final: 85 residues processed: 747 average time/residue: 1.6457 time to fit residues: 1559.7192 Evaluate side-chains 745 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 652 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 101 MET Chi-restraints excluded: chain Q residue 23 ARG Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain S residue 64 LEU Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain c residue 32 LYS Chi-restraints excluded: chain d residue 14 ASP Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 521 SER Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 326 optimal weight: 1.9990 chunk 525 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 365 optimal weight: 0.9990 chunk 550 optimal weight: 5.9990 chunk 507 optimal weight: 0.0040 chunk 438 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 338 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 75 GLN E 120 GLN F 121 ASN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 88 GLN L 5 GLN R 57 GLN R 78 ASN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 GLN ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69816 Z= 0.159 Angle : 0.583 9.954 101585 Z= 0.301 Chirality : 0.037 0.323 12438 Planarity : 0.004 0.063 7352 Dihedral : 23.547 179.434 28453 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 2.80 % Allowed : 25.57 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4112 helix: 1.02 (0.14), residues: 1387 sheet: -0.71 (0.20), residues: 707 loop : -1.19 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 438 HIS 0.004 0.001 HIS N 31 PHE 0.013 0.001 PHE J 97 TYR 0.017 0.001 TYR B 11 ARG 0.013 0.000 ARG T 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 693 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.3683 (tmm) cc_final: 0.3044 (tpt) REVERT: C 145 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7773 (ttt90) REVERT: D 70 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8787 (mt) REVERT: E 123 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: F 185 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8795 (t) REVERT: K 93 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: L 131 GLN cc_start: 0.8550 (tt0) cc_final: 0.8322 (tt0) REVERT: M 26 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6776 (mm) REVERT: R 56 ASP cc_start: 0.8440 (m-30) cc_final: 0.8237 (m-30) REVERT: S 6 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8546 (pt) REVERT: S 50 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7595 (mtm180) REVERT: S 66 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8084 (mtm180) REVERT: T 23 GLU cc_start: 0.5480 (mp0) cc_final: 0.4828 (mp0) REVERT: Y 10 MET cc_start: 0.8212 (mmm) cc_final: 0.7614 (mmp) REVERT: Y 19 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7461 (mptt) REVERT: b 122 MET cc_start: 0.0014 (ptt) cc_final: -0.0215 (ptt) outliers start: 99 outliers final: 62 residues processed: 752 average time/residue: 1.6450 time to fit residues: 1568.2135 Evaluate side-chains 733 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 662 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 101 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 66 ARG Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain X residue 35 ASP Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 54 CYS Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 553 random chunks: chunk 348 optimal weight: 10.0000 chunk 467 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 404 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 439 optimal weight: 0.1980 chunk 183 optimal weight: 9.9990 chunk 451 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 75 GLN E 120 GLN F 192 ASN G 113 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN J 64 GLN J 108 GLN K 88 GLN L 5 GLN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 HIS R 57 GLN U 83 HIS ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107824 restraints weight = 89714.800| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.05 r_work: 0.2865 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 69816 Z= 0.255 Angle : 0.624 10.418 101585 Z= 0.322 Chirality : 0.040 0.339 12438 Planarity : 0.005 0.067 7352 Dihedral : 23.543 179.475 28453 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 2.85 % Allowed : 25.71 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4112 helix: 0.94 (0.14), residues: 1387 sheet: -0.69 (0.20), residues: 706 loop : -1.19 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 438 HIS 0.005 0.001 HIS I 48 PHE 0.017 0.002 PHE J 97 TYR 0.021 0.002 TYR X 55 ARG 0.013 0.000 ARG T 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21938.36 seconds wall clock time: 382 minutes 21.46 seconds (22941.46 seconds total)